SMTL ID : 3t9d.1

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and 5-(PP)-IP5 (5-IP7)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 25 residues within 4Å: Chain A: R.98, P.113, V.149, K.151, H.158, V.160, L.175, R.177, E.201, E.202, F.203, M.204, D.210, K.212, R.226, S.228, P.229, D.273, L.275, C.284, D.285, N.287 Ligands: I7P.2, MG.3, MG.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:K.151, A:H.158, A:H.158, A:R.177, A:R.177, A:E.201, A:E.201, A:M.204, A:D.210, A:K.212, A:R.226, A:D.285, A:N.287 Water bridges: A:Y.102, A:R.226, A:R.226, A:S.228, A:S.228, A:N.287 Salt bridges: A:R.98, A:K.151

1 x I7P: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate(Non-covalent)

I7P.2: 13 residues within 4Å: Chain A: K.17, K.18, R.177, K.178, K.212, R.237, E.243, R.245, N.287, S.290, K.293 Ligands: ANP.1, MG.6 32 PLIP interactions: 32 interactions with chain A Hydrogen bonds: A:S.290 Water bridges: A:K.17, A:K.18, A:K.18, A:K.18, A:K.18, A:K.18, A:E.156, A:R.177, A:R.177, A:R.177, A:K.212, A:F.289, A:F.289, A:K.293, A:K.293 Salt bridges: A:K.17, A:K.17, A:K.18, A:K.18, A:K.18, A:R.177, A:R.177, A:K.178, A:K.178, A:K.178, A:K.212, A:R.237, A:R.245, A:K.293, A:K.293, A:K.293

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: D.285, N.287 Ligands: ANP.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.285, A:D.285, H2O.10 MG.4: 4 residues within 4Å: Chain A: D.273, D.285 Ligands: ANP.1, MG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.273, A:D.285, H2O.7 MG.5: 3 residues within 4Å: Chain A: S.32, F.34, I.37 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.34, A:I.37, H2O.7, H2O.8, H2O.12 MG.6: 1 residues within 4Å: Ligands: I7P.2 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.287 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat.Chem.Biol. (2011)

Release Date

2011-12-07

Peptides

Inositol Pyrophosphate Kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Inositol Pyrophosphate Kinase

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